Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20-27

Krishna Praneeth Kilambi, Michael S. Pacella, Jianqing Xu, Jason W. Labonte, Justin R. Porter, Pravin Muthu, Kevin Drew, Daisuke Kuroda, Ora Schueler-Furman, Richard Bonneau, Jeffrey J. Gray

Research output: Contribution to journalArticle

Abstract

Rounds 20-27 of the Critical Assessment of PRotein Interactions (CAPRI) provided a testing platform for computational methods designed to address a wide range of challenges. The diverse targets drove the creation of and new combinations of computational tools. In this study, RosettaDock and other novel Rosetta protocols were used to successfully predict four of the 10 blind targets. For example, for DNase domain of Colicin E2-Im2 immunity protein, RosettaDock and RosettaLigand were used to predict the positions of water molecules at the interface, recovering 46% of the native water-mediated contacts. For α-repeat Rep4-Rep2 and g-type lysozyme-PliG inhibitor complexes, homology models were built and standard and pH-sensitive docking algorithms were used to generate structures with interface RMSD values of 3.3 Å and 2.0 Å, respectively. A novel flexible sugar-protein docking protocol was also developed and used for structure prediction of the BT4661-heparin-like saccharide complex, recovering 71% of the native contacts. Challenges remain in the generation of accurate homology models for protein mutants and sampling during global docking. On proteins designed to bind influenza hemagglutinin, only about half of the mutations were identified that affect binding (T55: 54%; T56: 48%). The prediction of the structure of the xylanase complex involving homology modeling and multidomain docking pushed the limits of global conformational sampling and did not result in any successful prediction. The diversity of problems at hand requires computational algorithms to be versatile; the recent additions to the Rosetta suite expand the capabilities to encompass more biologically realistic docking problems.

Original languageEnglish (US)
Pages (from-to)2201-2209
Number of pages9
JournalProteins: Structure, Function and Bioinformatics
Volume81
Issue number12
DOIs
StatePublished - Dec 2013

Keywords

  • Binding
  • CAPRI
  • Protein docking
  • Protein interactions

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology

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    Kilambi, K. P., Pacella, M. S., Xu, J., Labonte, J. W., Porter, J. R., Muthu, P., Drew, K., Kuroda, D., Schueler-Furman, O., Bonneau, R., & Gray, J. J. (2013). Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20-27. Proteins: Structure, Function and Bioinformatics, 81(12), 2201-2209. https://doi.org/10.1002/prot.24425